A New Beginning
by crowned tiger
Summary: The old SHIELD has fallen, Hydra has returned. Coulson and May seek to rebuild SHIELD, train Skye and Jemma, help Fitz recover, and recruit former agents to defeat the threats to humanity and defeat Hydra. Meanwhile Coulson has to step into his new role as Director, while May steps up as Skye's new S.O. Both try to keep their team as the family they've grown to become.
1. Chapter 1

Author's Notes: This is my none age-play version of my story A New Beginning.

Thank you to everyone that convinced me to write this story :)

Chapter 1

"So where would you like to start?" Agent Billy Koenig asked. Coulson, May, Skye, Trip, and Jemma watched Koenig before looking around at the massive base.

"Wow." Skye whispered to Jemma.

"You should see the Medical Bay." Jemma answered. "It's like a mini hospital."

Coulson turned to face his team, "May, you and I will follow Koenig." He turned to Jemma and motioned to Skye and Trip with his head, "Will you take them to Fitz? We'll join you soon." He said putting an arm around Jemma as May nudged Skye towards Jemma's direction.

"OK" Jemma said quietly leading Skye and Trip to Medical Bay.

"Let's see what Fury left you, Director." May said turning to follow Koenig.

As Coulson's first order as Director he told Koenig to give Agent May a lanyard, and to give one to Skye, Trip, Jemma, and Fitz once the tour was over. Koenig quickly procured a lanyard for Agent May, then lead the two agents through the base. He showed them an exercise/training room that was filled with sparring mats, mirrors, exercise equipment, and weights, a kitchen, a common area room, barracks, bathrooms, a big garage, storage, a science lab, a medical bay, two offices, at least 8 vaults, and another large room that looked similar to a garage, Koenig explained that it was a simulation training room.

"This is impressive." May commented as Coulson looked around in slight awe. She nudged Coulson in the shoulder, "Are you finally speechless?"

"Um…" Coulson murmured as Koenig began to speak again.

"Before Fury went back into hiding, he alerted me that you would be arriving. The base has been equipped to assist the both of you in rebuilding SHIELD. We currently have limited resources but we do have some finances available and…"

"The rest we'll have to pick up as we rebuild." Coulson finished. "Do I get an office?"

"Of course Director!" Koenig turned and opened the door to the largest office, "All ready for you Sir. I have all the files that were at the Triskelion, the Hub, Providence, your Bus, and the Academy."

"And I have everything Fury gave me in this." Coulson said holding up the cube.

Koenig nodded, "If you need anything else Director? Deputy? I'll be in the storage room continuing to go over inventory. I should have a full report for you tomorrow."

"Thank you Billy." Coulson said as May gave a small smile watching Agent Billy Koenig leave.

"Well?" Coulson asked May. "Comfy chairs!"

May rolled her eyes, "We need to go check on Fitz. Then we should talk over things tonight, then make decisions tomorrow." May said heading to the door with Coulson following her.

AOS AOS AOS

Fitz lay in the Medical Bay. Unconscious. The only sounds were the beeping of the pulse, the sounds of the breathing tube, and other sounds that one would hear at a hospital. _Hospitals always freak me out._ Skye thought before her attention fell on her friend, the man she considered to be a brother lying like a ghost in bed. _This hurts too much!_ Skye thought closing her eyes feeling her heart break for Fitz but also for Jemma. She was finding it difficult to breathe. She suddenly felt very claustrophobic. She put a hand on her stomach. Remembering when Quinn shot her.

She jumped when Jemma placed a hand over hers, "It's alright." She said gently, "Even Medical Bays can be pretty upsetting." Jemma sat in the chair on Fitz's right, Skye followed Jemma's lead, grabbing a chair and sitting on his left.

Trip stood at the end of the bed, "Come on Man, pull through." He said quietly patting Fitz's leg. _I really want to break Ward's neck! Fitz doesn't deserve this_! He thought clenching his fist at his side.

Jemma looked across the bed at Skye. Skye looked at Jemma both holding one of Fitz's hands. "He'll be OK." Skye said in a whisper.

Jemma gasped as her eyes began to fill with tears, "He has to be OK! I just want my best friend back!"

Skye felt tears from her own eyes. She squeezed Fitz's hand tight, "Please wake up. Please be ok!" She whispered over and over as she and Jemma continued to cry for their friend.

Trip put a hand on Jemma's shoulder, "He'll pull through." He told them. "You'll see. He's tough."

"No he's not!" Jemma turned her voice hoarse from crying. "He was never in the field, we technically failed our Field Training. He wasn't tough enough to be caught in a situation like this! He just...he…" Jemma gasped.

Skye hid her face as her tears began to flow quicker down her face. She tried to take a deep breath and lifted her face from her hands. She looked around. _The noises! _ She thought as she glanced at all the machines attached to Fitz. _They're too loud!_ She thought anxiously as Jemma's cries were gut-wrenching. _I need to leave! I need to hide!_

Trip turned to see Skye jump out of her chair and race out of the room, "Skye?" He called while hugging Jemma trying to soothe her.

AOS AOS AOS

Shortly after Skye left, Coulson and May stood at the entryway to the Medical Bay. Coulson sighed. His face mirrored May's. Both of them concerned for the young agent and furious with Ward. "He's just a kid." Coulson whispered saying the exact same thing that May said about Jemma months ago.

May took hold of Coulson's hand and squeezed it, "They were all kids."

"We should have prepared them better!" Coulson said angrily staring at the young man in the bed. _I should order for Ward's death now!_ He thought angrily making a fist with his right hand, his nails digging into his skin.

May pulled at Phil's right hand to get him to release his fist. "We can now. You're Director and I'm Deputy, we can train them better."

"But is it too late?"

"If Fury thinks you can rebuild SHIELD, then it's not too late Phil." May said putting a hand on his shoulder walking past him, relieving Trip from holding Jemma and putting a comforting arm around her shoulders.

Jemma froze. She was slightly in shock at May actually showing her affection. But then she realized that's what she needed, _May was always protecting them, and when May wasn't there Fitz got hurt. I hope May killed Ward._

Coulson moved closer to Fitz's bedside, taking Skye's place. He gently squeezed Fitz's hand. He looked around, "Where's Skye?" He asked Trip.

"She left. I think everything was just too much for her." He said still looking at Fitz.

May let go of Jemma, "I'll go find her. You go and eat." She said to Jemma, "You look like you haven't eaten anything today." Jemma nodded following May out while Coulson remained with Trip and Fitz.

"Once you've finished eating, I want you to meet Coulson and the others in the common area on the Bus." May told Jemma.

Jemma nodded finishing putting a sandwich together and grabbing a Pepsi, "Alright." She said taking a bite and sitting at the table.

May nodded happy to see Jemma eating. She went to go find Skye. She had a pretty good idea where she might be too...

Skye was hugging her legs to her. After seeing Fitz lying broken in the Medical Bay of the new base, after seeing Jemma crying at his bedside, _It's too much_. She thought from the safety of her bunk on the Bus _Hydra needs to be gone! Ward is not supposed to be Hydra_. _He's disgusting! He's a murder! A Traitor! He almost killed FitzSimmons, he killed Victoria Hand and Eric...he wanted to take me! He is disgusting!_ Skye cried angrily into her legs. _I've should have known better!_ She thought wiping away a tear. _I should have known this was too good to be true._

"Skye?"

Skye lifted her head up and hastily wiped away any tears. She looked up to see Melinda May staring at her at the entrance to her bunk. "Yeah?" She asked her voice hoarse.

May entered and knelt down in front of the girl sitting on her bed. "We didn't get to finish our talk in the motel."

Skye looked down away from May's eyes, "I don't want to talk about it. SHIELD is gone! Fitz is laying in the Medical Bay in a coma which if he wakes up he will have permanent brain damage!" Skye's voice began to rise filled with anger, pain, despair. "I had a family, I _finally _ belonged somewhere and now it's gone."

"Skye it's not gone. It will never be gone."

"But SHIELD…"

"SHIELD is not gone. Coulson and I spoke with Fury. Coulson is the new Director and I'm his new Deputy." Skye's mouth widened in awe, "We're going to rebuild SHIELD, we're still going to be a foundation based on protection and we will defeat HYDRA."

"Coulson's the new Director? I guess I can't use A.C. anymore." Skye said a bit of her sarcastic and fun nature reemerging.

May smirked, "You may have to go with Director, or Coulson…"

"Or D.C." Skye paused at that, "Not sure that I like that sound, maybe I need to mull it over in my head."

"Skye, I meant what I said. This family is never gone."

Skye looked down, "I'm just so used to…"

"I know. I know you're used to be people abandoning you. People you thought was family, but look around, I'm right here. Trip is here. Jemma and Leo are here too. Coulson is here. We didn't and won't abandon you. So don't leave us, plus if you leave then how am I going to make you a SHIELD Agent?"

Skye blinked, "Are you serious? I thought you were just offering to be nice and because of Ward."

"When have you known me to joke?"

"Fitz. Everyone blamed me, but I know it was you."

May rolled her eyes, "Fine I give you that. I pranked Fitz. I wasn't just being nice. I want to train you."

"Why? I could barely defend myself and it took Ward a whole year to train me."

"I don't think Ward was really trying to train you. I think you were just another means for him to use while undercover." May told her truthfully. "But you've improved a lot since you met Coulson, FitzSimmons, and me."

"Do you think I can be an Agent?" Skye asked almost afraid of May's answer.

"I think if you had the right SO, the one that can teach you how to use all your strengths, improve on weaknesses, defend yourself and others, and be the support structure that you need mentally and emotionally to help you handle situations and emotions, then yes I think you'll be a great Agent."

Skye stared at her in awe, "I uh, I think that's the most I've ever heard you say to me. Or anyone say about my abilities and my personality."

"Everything I said is true. Coulson saw it, I initially saw it too, but I didn't want to. But now, SHIELD needs to be rebuilt and you need guidance. I want to be your SO. I can be that SO for you." May held out her hand, "What do you want?"

Skye took May's hand, "I want to learn from you."

"Good. We have to go to the common area of the Bus. Coulson and I need to address the team. After that, we need to talk a bit more." May said helping Skye up from the bunk and leading her out to common area.

When they arrived they saw Coulson standing, while Trip and Jemma were seated in front of him. "Skye take a seat please." He gestured to a chair. He wanted for Skye to sit before he began. He held up the cube that Fury gave him.

"What is that Sir?" Trip asked looking at the cube.

"This is the key given to me by Fury. Yes Fury is alive, but in hiding. This Trip, Jemma, Skye is the key for me to rebuild SHIELD and fight Hydra." Jemma gasped while Trip smiled and Skye glanced over to May. "With this key I've been made the new Director of SHIELD and I have made May my Deputy. Now rebuilding SHIELD, fighting Hydra, protecting people is going to be difficult. We've already been hurt by ones we thought were friends. We're already small, but I want to make SHIELD what it once was, an organization whose purpose is protection." Coulson looked at each of them in the eyes, "If any of you want to leave, to return home to your family we won't think any less of you, but I would like you all to help May and I to rebuild SHIELD."

"I'm a Legacy Sir. I'll definitely help you rebuild." Trip said standing up at attention.

"I'll help D.C." Skye and Coulson paused while May rolled her eyes, "Yeah I'll try to work on a new nickname, it definitely doesn't fit."

Coulson turned to Jemma who was looking at her hands. "Jemma." He whispered kneeling before her, "I know you've been through alot. If you wish to leave, I won't hold it against you. None of us will."

"I'll stay." Jemma said looking up. "I'll stay Sir." She said raising her head and sticking out her chin in determination.

Coulson nodded, "Alright. Work begins tomorrow."

The others nodded, "I'm going to go sit with Fitz some more." Jemma said leaving the room.

"Any orders for me Sir?" Trip asked stepping forward.

"Go enjoy a bag of chips Trip, you can explore the base, Billy is supposed to give you a new lanyard." Coulson told him with a grin.

"Yes, Sir." Trip said.

Coulson turned to Skye, "So May is your new SO now?" Skye nodded stealing another glance at May. "Good. She'll be good for you." He said smiling at May.

Skye nodded, "I think I'm going to go try to find something to eat. Um, May? Do we start tomorrow?"

"Tomorrow you along with Jemma and Trip will help Coulson and I with organizing and paperwork, we might start tomorrow evening, but actual training will probably begin the day after tomorrow." May told her.

Skye nodded, "Alright." Skye left to get food.

May turned to Coulson, "We should probably start some this evening."

"Agreed." Coulson said as the two headed out of the Bus, "But let's eat first. I'm famished."

Once they were done eating, they went to Coulson's new office and started to go over files, intel, etc... that Fury left for them. "Are you just inherently good at everything?" Coulson asked after a hour of organizing paperwork.

May looked up, "Meaning?"

"Martial Arts, you had our class beat out on the day you arrived, piloting, espionage and now you're filing and organizing like a pro. What are you not good at?"

"Spotting hidden Hydra Agents?" May said angrily.

"That wasn't your fault, Melinda." Coulson sighed, "We were all betrayed."

"I know, still doesn't mean I'm not angry." May said siding aside a stack of folders and putting it in the filing cabinet.

"Speaking of things that will make you angry," Coulson said nervously dreading to bring this up, "I'm having Ward moved to our custody. Koenig said that Fury had a few of the vaults turned into cells."

May made a sound very similar to a growl, "Why?" She snarled although she pretty much already knew the answer.

"Intel on Hydra." Coulson said confirming her suspicion.

"When?"

"In three days." He said putting another stack of files into the cabinet.

May nodded, "Skye, Jemma, and Fitz can't know."

"Agreed." Coulson said stretching his back, standing up. "Call it a night?" May nodded, "Great."

AOS AOS AOS

Coulson looked around. _What woke me up? _He thought glancing around the darkness. _I think I'll get some water. _ Once he finished taking a drink he thought of walking around the base again. He went to the storage area and found the markings that Garrett drew.

Coulson reached out and touched it. He blinked as a flood of images filled his brain. He walked by the drawing and picked up a pocket knife. He stared at the blank wall in front of him. _It must be carved. _He stared at the wall, "It must be carved." He said quietly as he began to sketch symbols into the wall.

It took hours but suddenly the compulsion to carve went away. Coulson gasped as he moved away from his carving. _I have to go get May. _He thought walking away, locking the door behind him.


	2. Chapter 2

Author's Notes: This is my none age-play version of my story A New Beginning. That version is on Archive

Please note, I have a 3 month old son, so my time is very much devoted to him. I will do my best to update as my time permits :)

Chapter 2

May had always been a light sleeper, being raised by her mother and trained as a specialist for SHIELD. She inherently became ready for action at a moment's notice. So when she heard pounding on the door, it didn't take long for her to grab the ICER on her bedside, jump out of bed, and open the door at the ready. "Phil?"

Coulson was staring at her. May had never seen Phil look at her the way he was looking at her now. He was heavily breathing, his eyes wide with fear, but when he spoke he was eerily calm, "It's begun." he said.

May instantly dropped the ICER and moved aside for him to enter. "When?"

"Just now, I saw the drawing that Garrett did. It triggered something, and I just needed to…" Coulson trailed off, staring at his hands.

"Needed to what?" May grabbed Coulson's hand, "Phil?"

"I needed to carve." he answered.

"Show me."

May followed Coulson to the storage room where Coulson had been for most of the night. She looked in shock at the carvings on the wall. "What do I do?" Coulson looked at the person he trusted most, "I was just made Director… and here I am going insane?"

May took out her phone and took pictures of the carvings. Once she finished, she turned and searched the storage until she found some plaster and a scraper. She mixed the plaster together and set to work to repair the wall. Coulson grabbed another scraper and followed suit.

May turned her attention back to Coulson. "Follow me." She said when they finished.

Coulson followed May back to his room, "Aren't we going to discuss what just happened?"

"Yes, but Phil, you're exhausted and you're emotional. We don't want to make decisions based off our emotions, especially fear. I'll fix you some tea, stay with you tonight, and in the morning we'll figure something out." May told him as she helped him sit in his bed, "I'll be right back."

Coulson tried to relax while he waited for May to return. Skye has the GH serum too, he remembered with sudden anxiety. He took the tea May gave him and sipped, "Thank you."

May nodded. She watched her friend calm and relax. "Rest."

Coulson nodded, setting the empty cup on the table by his bed, "We'll discuss this first thing in the morning." He said lying down.

"Yes, we will." May said, sitting beside him, watching him sleep. She kept the ICER at her side, just in case.

* * *

><p>May awoke just an hour and half later, it was around 4:30 am. She glanced at Phil, got out of bed, and went back to her room. She took a quick shower, put on civilian clothes, and texted Agent Koenig. May was out of the barracks and in the garage by 5 am, getting in one of their black sedans and driving away.<p>

She drove into town and made her way to a local 24 hour gym in town. She walked in and made her way towards the woman's locker room. She found the locker and pulled out the black bag inside and shut the locker door, locking it again.

On the way out May took a good look at the facility, "I can bring Skye here to train on some days." May said to herself, leaving the gym. Once she got back into the sedan, she opened the bag that revealed a passports, money, fake I.D.s… She sent a text to her mother and started the sedan driving back to the Playground.

* * *

><p>Coulson woke at 6:30 am, got up, showered, and dressed in his suit. He went up to his new office, but first he stopped to grab a coffee. Upon entering, he saw May waiting him. "Morning." He greeted.<p>

"Here are my terms: No more field missions, and you check in with me every few days. You're in charge of SHIELD, but I'm in charge of you." May told him, "Other than that, I have your back and am ready to help you rebuild SHIELD. Do you accept?"

Coulson blinked, "That's it?"

"For now, yes."

"Yes, but what about Skye? She also has the GH serum." Coulson reminded her walking around May and sitting in his chair.

"I'm her new S.O. Let me monitor her as she trains; we'll watch her on the security feeds."

"You came up with all of this just between now and 2 am last night?" Coulson asked incredulously.

"I told you: tea helps." May replied.

Coulson nodded, "When should we introduce her to the carvings?"

"Not yet, let's wait and see how you do, and how she does with training. We don't want to overwhelm her,." May suggested. "I'm going to go wake up Skye, and make sure Jemma actually slept. Meeting in 20?"

Coulson nodded, "Yes."

* * *

><p>"Alright, good morning everyone." Coulson greeted as Koenig, Trip, Skye, Jemma, and May entered his office. "Here's the itinerary for today," he said, handing out assignments, "Trip, your job is to gather all the reports and curriculum from the Academy of Operations, then I'd like you to put together a list of possible candidates, former agents, and legacies of SHIELD for recruitment."<p>

"Yes Sir," Trip said taking his folder.

"Koenig will direct you to your resources. Once you've finished turn the Academy reports to Agent May and the recruitment list to me."

"Yes Sir." Trip said again.

"Skye," Coulson turned his attention to Skye, "I want you to go through SHIELD's Academy of Communication, gather the curriculum and other teaching guides, then I want you to gather and update the Gifted Index. Once you've finished report to May."

"Got it," Skye said taking her folder with a smile. "I mean-sure. I mean- yes Sir?"

Coulson shook his head at Skye's confused answer. He handed a folder to Jemma, "I want you to go with Koenig over inventory that you will need for the science labs, then the curriculum of SHIELD's Academy of Science and Technology. When you've finished you can return to Fitz if you wish."

Jemma took her folder, "Thank you, Sir." she said with a small smile.

Koenig stood up, "If you all would follow me." he said leading the young agents out to do their tasks.

* * *

><p>Coulson woke at 6:30 am, got up, showered, and dressed in his suit. He went up to his new office, but first he stopped to grab a coffee. Upon entering, he saw May waiting him. "Morning." He greeted.<p>

"Here are my terms: No more field missions, and you check in with me every few days. You're in charge of SHIELD, but I'm in charge of you." May told him, "Other than that, I have your back and am ready to help you rebuild SHIELD. Do you accept?"

Coulson blinked, "That's it?"

"For now, yes. Those are my terms, acceptable?"

"Yes, but what about Skye? She also has the GH serum." Coulson reminded her walking around May and sitting in his chair.

"I'm her new S.O. Let me monitor her as she trains; we'll watch her on the security feeds, and we'll slowly introduce her to the carved images."

"You came up with all of this just between now and 2 am last night?" Coulson asked incredulously.

"I told you: tea helps." May replied.

Coulson nodded, "When should we introduce her to the carvings?"

"Not yet, let's wait and see how you do, and how she does with training. We don't want to overwhelm her,." May suggested. "I'm going to go wake up Skye, and make sure Jemma actually slept. Meeting in 20?"

Coulson nodded, "Yes."

* * *

><p>"Agent May?" Trip knocked on May's office door.<p>

"Come in Trip." May answered. She was on her laptop.

"I have the curriculum from Academy of Operations." He said setting down a few USB drives, "I marked which are for Field Agents and which are for the Specialists." He glanced down at her tablet, "Is that the curriculum from yours and Agent Coulson's Academy years?"

May nodded, "Yes it is. We kept ours in case. A few times I was called in to help teach a class." She took one of the drives and plugged it into her computer, "Have you done your recruitment list?"

"No that's next on the list. I was going to prepare lunch, if you want any?"

"Thank you Trip. How are the girls?"

"When I walked past they were still going through the other curriculums."

May nodded, "Thank you." She glanced behind him to make sure the door was closed, "In two days we're going to have a prisoner in one of our cells."

"Agent Ward?" Trip answered.

"Yes, I need to be there when he's brought in. I will be training Skye by that time. When Ward comes I need you to supervise Skye while I help Coulson."

"Yes Ma'am." May gave him a look, "I mean, copy that."

"Thanks, I don't think I'm ready to be addressed as 'Ma'am' yet." May told him with a look.

"Do you need me to do anything else once I finish my list for Coulson?"

"Help me prepare the training room." May said going back over the Field Agents' curriculum, "I'd like you to assist in Skye's training some days, otherwise Coulson and I will give you assignments."

"Copy that," Trip said, leaving May's office.

* * *

><p>It wasn't until 8:30 pm that Skye finished her assignment. She yawned as she turned in her USB drives. "Don't forget to report to Agent May." Koenig reminded her beginning to take inventory on what Skye had brought him.<p>

Skye grimaced, "I'm so exhausted from staring at the computer all day."

"I bet," Koenig sympathized.

Skye sighed and walked away. She first knocked on Coulson's door, when she realized May wasn't there she went to find her S.O.'s office. She knocked, "May?"

"Come in," May called back. "Thank you, yes I'll retrieve them in four days. Bye." She hung up the phone as Skye timidly entered her office. "Good evening, Skye."

"Hi," Skye said nervously, "Are we beginning tonight?"

"Have you had dinner?"

Skye froze, "Dinner?"

"Did you have dinner yet?" Skye shook her head, "Alright, well, let's go and eat. This will count as your first meeting with your S.O." May said standing up bringing her tablet, "Make sure you grab your tablet too."

Skye nodded. As she followed May to the kitchen. She took in a deep breath. She anxiously waited what May would do next. "What do you want me to do?" Skye asked.

"Grab some plates and silverware." she said cryptically.

Skye set her tablet down and gathered silverware and plates. She turned around to see May setting food on the table, Mexican food. "When?"

"Are you just going to stare or are you hungry?"

Skye hastily set the plates down with the silverware and gathered food to her plate, "Seriously how? We're in a hidden base!" May gave Skye another one of her 'looks,' Skye nodded and began to eat.

As Skye continued to eat May sat across from her and prepared a plate for herself, "I've made a syllabus for you." She began, "Check your email, I sent it to you before I left the office."

Skye pulled out her tablet and opened the email from May. Skye read her schedule that May had prepared for her:

"7 Am-10 Am: Conditioning drills

7 Am-7:15 Am: Warm Up jog and Yoga

** Beginning in two weeks Tai Chi

7:15 Am-10 Am: Conditioning

Stretching

Running-Long Distance running and Sprinting

Split into Light, Moderate, and Intense

Exercises- Pull-ups and Push-ups

Weight lifting

9:45 Am-10 Am: Cool down and Yoga

1 Pm-4 Pm: Fundamentals, History, and Exams

Mondays and Wednesdays focus: Combat and survival

1 Pm-2:30 Pm: Combat: Hand-to-Hand Combat

**Beginning week 5 Weaponry

2:45 Pm-4 Pm: First Aid

**Beginning in 3 weeks Survival

**In 8 weeks Search and Rescue/Retrieval

Tuesdays and Thursdays focus: Automotive Electronics

*Beginning in Week 3 Espionage

5 Pm-8 Pm: Practicum Labs

Mondays, Wednesdays, and Fridays:

5 Pm-7:45 Pm: Combat drills

**Wednesdays:

5 Pm-5:15 Pm: First Aid

5:15 Pm-7:45 Pm: Combat drills

7:45 Pm-8 Pm: Cool Down

Tuesdays and Thursdays:

5 Pm-8 Pm: Automotive Skills

**Some class periods will take place in the evenings.

**You will still have be approved for actual assignments

** In 2 months you will participate in simulation assignments these are your practical exams"

Skye's heart constricted as she read her schedule. She swallowed hard, her food forgotten on her plate, "This is a lot." she told her anxiously. "I'm…"

"You can handle it," May told her firmly. "You've shown dedication in wanting to be a SHIELD Agent. I know that you'll succeed."

Skye was looking down at her tablet. She had opened May's nutrition document, apparently changing her diet as well, "How…"

"Skye, look at me." Skye looked up at May, her tone suddenly gentle. "You can do this. I'll be with you every step of the way."

"OK," Skye said she fidgeted with her silverware, "Can I go keep Jemma company?"

"Finish eating first. I'll wake you up at 6:30 Am tomorrow. Meet me in the kitchen for breakfast."

"OK." Skye nodded eating her taco.

* * *

><p>Skye found Jemma sitting at Fitz's bedside. "Jemma?"<p>

Jemma hastily wiped her eyes, "Hello Skye."

"Do you need some company?" Skye asked from the doorway.

"Yes, I'd appreciate that."

Skye moved to sit on Fitz's otherside, "Any news?"

"The longer he sleeps… they're positive he'll have some brain damage. He was without oxygen way too long. He's now been asleep for 3 days." Jemma explained wiping her eyes again, "Excuse me." She said hastily trying to stand.

Skye grabbed her hand, "It's OK. You're allowed to feel, Jemma." She said moving to hug her friend.

Jemma hugged Skye back, "Thank you."

"Have you ate yet?" Jemma shook her head, "May got Mexican food," Jemma looked at Skye with a shock expression, "I know don't ask how, there's still some food left." Jemma nodded letting Skye lead her away from the Medical Bay.

Both girls were shocked to find a plate out and waiting for Jemma. "How did you do that?" Jemma asked Skye taking a seat.

Skye shrugged, "It wasn't me!" Out of the corner of her eye she say May walk past the door, How does she know? How does she do that?

As Jemma began to eat, Skye sat across from her nibbling at a chip or two. "How do you feel about May being your new S.O.?"

"Scared actually no, terrified! She never really seemed to care a lot about me before and now she's my new S.O. How will she train me? I mean at least, well I thought Ward cared." Jemma flinched at Ward's name. "Shit! Sorry Jemma I didn't think."

Jemma looked up, "No Skye it's alright. I'm fine. Jemma paused before continuing, "Did you know she pummeled Quinn when you got shot?"

Skye's eyes widened in shock, "She did? You mean May, right?"

Jemma nodded, "She…, during the whole time while we waited at the hospital for you, she was reassuring all of us, that it was Quinn's fault and no one else. Then when the doctor came to talk to us…" Jemma took a breath, "She was so angry at what the Doctor said, she left...and tore up Quinn's face."

"She did that?"

Jemma nodded, "That's why when the whole thing with her and Coulson...and even everything else. I...I knew...I just knew that she cared for all of us, probably more than we'll ever know."

"I just...the last time I called someone 'Mom' they sent me back…" Skye mumbled looking down.

Jemma reached over and took Skye's hand, "You really think Coulson and May would send us back?"

"You need to talk to them too." Skye said squeezing Jemma's hand.

"I know." Jemma said smiling at Skye and going back to eating.

* * *

><p>May watched Skye head out to the Bus. She followed her. She watched Skye bury herself under the warmth of multiple blankets. "Skye?"<p>

Skye's figure jumped, "Geez! Don't do that!" She said pulling head out of her cocoon. "Is something wrong?"

"Want to come inside the base? It's warmer there?" Skye shook her head. May nodded, "Alright then." She pulled out another blanket and placed it on Skye, "After we start training I want you to stay in the barracks."

Skye sighed as another warm blanket was placed on her, "Alright." She watched May settle in beside her, "You're staying?"

"You could use the company."

"May?"

"Yes, Skye?"

"Thank you for pummeling Quinn for me."

Skye felt May squeeze her hand as she closed her eyes with a grin.


	3. Chapter 3

Author's Notes: This is my none age-play version of my story A New Beginning. That version is on Archive

Oops Disclaimer: I don't own Marvel or SHIELD

Chapter 3

Wednesday, Day 1 Training

6:30 Am

"It's time to wake up Skye." May gently shook the girl. She was up at her usual 5 Am time preparing for Skye's first day of training.

Skye groaned, "Do I have to?"

"If you want me to train you, yes." May said, "I found a few old uniforms of SHIELD's for you to wear."

"Thanks," Skye said sitting up, "This is similar to what you wear," she commented on the outfit.

"They are easy to move in. Meet in the kitchen at 6:50, that gives you 15 more minutes to get ready."

Skye got up and put on the outfit that May got for her. She was wearing black yoga pants, and a top that could easily be turned sleeveless if needed, with the SHIELD symbol on the shoulder in silver. Skye ran into the bathroom and quickly brushed her hair then her teeth and put her hair in a ponytail.

May looked up as Skye entered the kitchen, "I made you a breakfast shake. Once you're done drinking we'll start our warm up jog, stretching, and yoga."

"OK," Skye said drinking her shake, "May I'm nervous."

"I know, I'm going to train you hard, but the important thing is you do your best." May led Skye to the exercise/training room. "After we warm up we're going to do some long distance running."

"In a warm up jog you're not trying to go too fast or move too quickly, it's just to warm up your muscles." May instructed jogging along with Skye.

"So this is basically like a fast walk?"

"Basically, good. Let's go down this hallway," May said leading. After the warm up, May led Skye through stretches and yoga. May taught her how to stretch her muscles effectively, she wanted to make sure Skye stretched her muscles the right way, to eliminate possible injuries. "Good, count to 8, deep breath, good, now release." She said leading the stretch.

Once May and Skye stretched, she pulled out a map of the base, "This is your route for your long distance run, it will give you a chance to map out the new base. As you run I want you to work on managing your speed and paying attention to your surroundings." Skye nodded taking the map, she turned to start running, "I'm coming with you." May said.

After their long distance run, May helped Skye to stretch a bit more, "Tell me about the base, what did you see?" she asked. "Can you give me any details?"

Skye answered the best she could as May helped her stretch her hamstring, "It seems the corridors have color coded signs."

May nodded her head in approval, "Very good, now it's time for exercise. Go grab a drink of water first."

After Skye's break, May led Skye in vigorous exercises: lunges, wall sits, pullups, pushups, the plank position, every exercise to work out her muscles and build strength. "Now I'm not trying to turn you into a body builder, these exercises are for you to be capable and strong enough to work our equipment and weapons, and to build your endurance so you don't get too tired on missions." May explained while Skye did lunges.

"OK," Skye replied trying to focus on the correct form.

"You're going to be sore tomorrow, the next day, and the next day. Stretching is very important." May said leading Skye through the next exercise. "This will help you learn to process and manage pain."

Skye was breathing hard, "Right, because if I'm hurt on the field, I won't be able to suddenly take a break."

"That's right, you'll need to get somewhere safe, or go dark." May explained, "Speaking of which, you need a water break, when you come back we'll do sprints, stretch again then go on a 10 minute break."

After Skye's break, she returned to the training room to find Trip there, "Hey!" she greeted.

"Hey girl!" He said with a grin as May turned to them, "Ready for sprints?"

Skye nodded as May led Trip and Skye through sprints. Skye was exhausted after ten minutes of sprints. "Good job, Skye." May nodded going over to her, "No! Don't bend down, keep your arms up and keep walking around." May maneuvered Skye's arms to behind her head, "That's it, good."

Skye got another break, then she and Trip did some weight lifting, May observed so Skye could properly lift weights without hurting herself. May checked the time, "Alright, Skye it's now 9:45 do your cool down jog, which is similar to your warm up job, then stretch. Once you're finished go check in with Coulson, meet me here at 1 pm, don't forget to eat lunch, I'll have a list of options for you."

"OK," Skye said doing her warm down jog.

Skye was very sore and tired by the time she made it to Coulson's office. She knocked and felt her muscles tense, "Sir?"

"Come in Skye," Coulson answered back as he was preparing his briefcase.

"Anything you'd like me to do?"

"Help Simmons prepare the barracks, make sure you eat some lunch though." He said packing his briefcase.

"Are you going some where?"

"Koenig found one of Field Agents, I'm going to meet them, see if they're interesting in joining SHIELD."

"Without backup?"

"I know this Agent, she's not Hydra."

"How do you know?"

"She was close to Victoria Hand. I'll only be gone 24 hours." Coulson said grabbing his briefcase. He turned back to Skye, "Don't worry."

Skye followed Coulson out of his office. She turned and headed towards the kitchen. She met May who was putting together a meal for Skye and herself. "Do you have orders from Coulson?"

"He wants me to help Simmons make sure some barracks are ready for any arrivals."

May nodded setting a plate down before Skye, "Alright, do what you can then meet me in my office."

* * *

><p>Skye found Simmons preparing a room. She entered, "Hey."<p>

"Hello Skye," Simmons greeted with a small grin.

"How is Fitz?"

"No change," she said sadly. "How's training with May?"

"Intense," Skye answered as they moved to the next room. "May said that I need to remind you to eat lunch."

"OK," Simmons said as she and Skye continued to work.

* * *

><p>1 PM<p>

Skye was sitting across from May in her office, "So we're doing combat and survival skills?"

"Today you'll learn about the history of Tai Chi." May answered sending an email to Skye, "I want you to read and research what Tai Chi is. As you read you will learn that it's not just a form of martial arts, but also a form of meditation and handling stress."

"Did your S.O. make you study the history of martial arts and combat?" Skye asked after 10 minutes of reading.

"My mother made sure that I studied all forms of combat before I began training. When I joined the academy I already possessed a few black belts."

Skye's jaw dropped in shock, "Wow."

"I was trained basically from birth Skye." May's tone held amusement.

"You're more than spy, you're like a ninja…" Skye mumbled continuing her reading.

May didn't answer, partly because her phone rang, "Hello? Yes we're safe. I was wondering do you know the last location of Bobbi? Have her call me when you find her, thanks Nat." May hung up her cell.

"Were you just talking to the Black Widow?"

"Study."

"Copy that." Skye said with a sigh.

At 1:35 May told Skye to take a small break. Once she returned May handed her a SHIELD first aid handbook. "Study." Skye nodded taking the book and going to read.

* * *

><p>5 PM<p>

At the start of the hour, May went over some first aid with Skye. She taught her how to wrap sprained ankles and create splints for possible broken arms or legs. She had Skye practice over and over after she would demonstrate.

May released Skye for a break around 5:20 Pm. "We're going to do a warm up jog and some stretching before we begin combat training." May told her as they started to jog.

"So are we beginning Tai Chi?" Skye asked once they were warmed up and stretched. I feel so stiff from this morning, Skye thought with some pain.

"Not exactly," May said moving Skye to the middle of the mat, "Tai Chi as you read, can be used for more than just combat, it's very healthy for you mentally as well as physically. There is a rule regarding Tai Chi, the 70% Rule. Do you remember what that is?"

"Don't push yourself, as you begin only do 70% of what you can do." Skye answered as May circled her.

"Very good." May stood before Skye, "What we're going to begin with the first week is energy awareness, breathing, and standing in neutral position."

Skye nodded as May showed her how to center herself, "Like this?"

May nodded, "Yes, now I need to know, do you still have nightmares of Quinn shooting you?"

Skye froze mid breath, "I um…"

"Tell me the truth, do you?"

"Sometimes," Skye said looking away, she didn't want May to know that she either had nightmares about Quinn shooting her, or Ward, or her foster homes. She didn't want May to think her weak.

May frowned. She recognized by Skye's posture and her breathing that she wasn't being completely honest. "Do you have other nightmares?"

Skye looked anxiously at her S.O. "Do we have to talk about this now?"

"Go take a break," May told her letting it go for now. She needed to find another way for Skye to share her feelings. She wasn't training a normal SHIELD Agent. Skye was still dealing with trauma from Quinn and Ward.

For the rest of Skye's training May had her do the Circling Hands exercise. At 7:45 May stopped Skye told her to do a cool down jog and stretch. At 8, May helped Skye up, "You did a good job today Skye."

"I did?"

"Yes, why don't we go eat dinner."

"I feel tired and sore." Skye mumbled trying to stretch a bit more.

"I know. You're going to be, but you can relax." May told her leading her out of the training room.

* * *

><p>Skye was sitting on her bed trying to relax when May entered with some ice, "We're going to ice your tibias for 15 minutes, then I want you to take some ibuprofen with dinner."<p>

"OK," Skye said watching May set the ice bags on her knees. "The ice is beginning to hurt." she said after a few minutes.

"I know, keep it there until I tell you to take it off. It will help with the soreness and prevent injuries." May said giving a gentle rub to Skye's shoulder. "Good girl, just relax."

Skye waited for 15 minutes then took the ice bags off. "Time for a hot shower." she said grabbing her towel. After her shower Skye toured the base until she found herself at May's office.

"Skye?"

"I dream about Quinn a lot." Skye said in a little voice. "And my foster homes from when I was little, and, um... Ward..."

"I know. Why didn't you tell me earlier?" May asked.

"I was ashamed."

"Never be ashamed for feeling Skye. What Quinn did to you was traumatic. To say you're not still affected would be unrealistic." Skye looked down. May walked to Skye and gently lifted her chin, "When you have these thoughts or dreams, regarding Quinn, or Ward, or your past foster homes, I want you to come and talk to me. Understood?"

Skye nodded, "OK."

"Go get some sleep Skye."

"Night May."

* * *

><p>Skye had difficulty getting up the next morning for training. She was so sore and tired. Her arms and legs were like jelly. She could barely lift them up, but somehow she managed to get through her conditioning training. After lunch she spent some time with Simmons at Fitz's bedside. When it was 1 Pm she went to meet May in her office.<p>

May let her in, "Skye I have the material I want you to read over about the our SHIELD sedans. The manuals are on the desk. Coulson's back and I need to go meet with him."

"Can I come with you?"

"No, but you'll probably see him tonight." May said rushing out to Coulson's office.

Skye huffed but went to do her studies.

May walked right into Coulson's office, "How did it go?"

"Hartley will join us. She knows where a few other agents are. Trip got ahold of few of his friends that trained with him to be specialists. They will arrive tonight." Coulson said loosening with tie.

"How do you feel. Is the compulsion back?"

"Not yet, I just hate coach. Plus it was difficult to tell Hartley about Hand." May nodded, "How's Skye's training?"

"So far she's doing well." May answered.

Coulson nodded, "Good. I have to go and speak with Koenig and prepare for Ward to come. Simmons said she found a few Scientists from the Academy still loyal to SHIELD. She's arranging a meeting for me with them."

May nodded, "Good."

* * *

><p><strong>Friday Ward's arrival<strong>

9 AM

Jemma knew Skye was training this morning, but she noticed how tense Coulson, May, and Koenig were acting. In the past few days Coulson, Koenig, and Trip were able to recruit some former agents and military personnel. Jemma watched as a few Specialist Agents stood at attention, weapons at the ready. She gasped when she saw a man in chains with a black bag over his head brought it. She recognized that body, "Ward." she whispered.

Ward was led through the base, bag preventing him from seeing anyone or anything as Koenig and Coulson directed the agents to Ward's cell. May walked behind the group then sighed when she saw Jemma, "Go wait for me in my office."

"Why?"

"Go wait in my office." May reiterated, turning Jemma towards her office and nudging her in that direction.

May turned her attention back to handling Ward. Ward was placed in the cell, "Hands." Coulson said.

Ward held out his hands. May walked over and pierced his neck with a syringe, a sedative. Ward began to sway as the agents moved him to his cot. The boots, socks, and shackles were removed. May turned to Coulson as he set up a chair, "Go see to Simmons."

* * *

><p>Simmons was pacing May's office, she couldn't believe it! Ward is here! In this base. Why is Ward here?<p>

"Jemma."

Jemma jumped. She didn't hear May enter the office. Once recovering from her shock she rounded on her Superior Officer, "Why is Ward here?!" May continued to look at Jemma. "Why?!" Jemma voice began to break, "HE SHOULD BE DEAD! HE SHOULDN'T BE HERE! HE…" she whimpered.

May caught Jemma and held her up as she almost collapsed under her weight of emotions, "You weren't supposed to find out yet. We need him here. We need his intel about Hydra."

"He almost killed me." Jemma whispered, "He almost killed Fitz. Fitz is still…"

"I know. I know." May put an arm around Jemma leading her to sit down, "I hate that he's here, but we're in the dark about Hydra and he's a possible way to get to them."

"I… I just don't want him here."

"We don't either, but sometimes we need to do what is needed and not what is wanted." May told her gently rubbing her arm in a soothing motion. "You don't have to have any interaction. OK?"

"OK."

* * *

><p><strong>Tuesday 9 days after FitzSimmons's Accident<strong>

Jemma was at Fitz's bedside. She didn't have any work to do at that moment, inventory was finished yesterday. She just needed to be with Fitz. She glanced at the clock, 11 Am. Skye would be on her break and getting ready for lunch.

Jemma debated joining Skye. Instead she moved her chair closer to Fitz's bedside. "Please wake up Fitz." she pleaded. She looked down when suddenly she felt pressure on her hand. Jemma gasped looking up to see Fitz slowly opening his eyes. "Fitz! Don't worry, just breathe." She said jumping up and checking his vitals. She couldn't believe he'd woken up: she'd begun to be afraid it would never happen.

Fitz stared at Jemma. He looked around his eyes wide with confusion. "You're alright Fitz, let me call the doctor." Jemma said pushing a call button. She felt tears pricking her eyes.

"Excuse me, Doctor Simmons," Fury's doctor said as he came over to check Fitz's vitals. He places his hand on Fitz's cheek, looking into his eyes. Fitz blinked, eyes falling shut again. "He's going to be tired and little confused," the doctor said in a reassuring voice. "But this is excellent progress."

"Is he alright?" Simmons asked anxiously as Fitz's eyes stayed closed.

"We'll know more the next time he awakens." The doctor said honestly. He made a few notes on Fitz's chart. "Please go inform the Director and the Deputy, you'll be back in time for him to wake up."

Simmons nodded hastily leaving the Medical Bay to find Coulson, May, and Skye…

* * *

><p>Coulson found May with Skye and Jemma that night in May's office. "I just spoke to the doctor. We know there's damage to Fitz's temporal lobe, but it will take a while to see how much it will affect him."<p>

"What are we going to do?" Skye asked.

May sat beside Jemma and wrapped an arm around her as she cried, "We should have thought of another way."

"Jemma this isn't your fault." Coulson said kneeling before her taking her and Skye's hands, "This is Ward's fault."

"We will help Fitz. This is our family." May told them. "He's still a part of SHIELD and we'll help him recover. Alright?"

Jemma nodded leaning her head into May's shoulder, "Alright." she hiccuped.

"Promise?" Skye asked leaning into Coulson.

"We promise." he said.

* * *

><p><strong>Monday, Day 8 Training<strong>

It had been 8 days since Skye begun training under May, 2 days since Fitz woke up, and last night she found out Ward was living in their basement. During the first 5 days of training Skye showed drive, ambition, and excitement to learn under May. However, the last three days, Skye was becoming more and more anxious and frustrated with her S.O.'s training methods and with information she felt is being kept from her.

May watched Skye repeat the Tai Chi sequence again, it was 1:15 in the afternoon and Tai Chi which is used in the morning as a warm up has now been added to their combat training in the afternoon. May sighed, Skye is not applying herself, like she did last week. May watched Skye's lack of focus on her form, she failed her quiz this morning. She watched Skye struggle with the sequence, she's already forgotten the next form. "Skye what's wrong?"

Skye paused "Nothing." she said trying to concentrate on the routine.

"Skye?"

Skye took a deep breath, "I don't want to disappoint you or Coulson." she whispered. Skye sat on the floor her head going to her knees, while her arms wrapped around them. She sniffled trying not to cry. She tried to breathe, She won't want to train me now. Skye thought ashamed at herself.

May walked over to her student and sat down in front of her, "Skye, do you remember what I said two weeks ago?"

"When we were on the Bus?" Came Skye's muffled reply.

"I told you that I wanted to be your S.O. I wanted to train you and that I thought you could become a great Field Agent." May gently reached over and unwrapped Skye's arms from around her knees, "I also told you I'll be your support structure, your support mentally and emotionally, remember?" Skye nodded still hiding her face from May. May reached over and gently lifted up Skye's chin, "Then talk to me."

"I dropped out of high school," Skye told her, "I was never good at taking tests and as we continue it's- I get anxious…"

"So written tests and quizzes cause you anxiety. Do you know why?"

"I used to think my grades were the reason I wasn't getting adopted and so I tried harder to be perfect in school and taking test, but more time passed and I was moving home to home and the tests became harder to do...finally I just couldn't…" Skye wiped her eyes, "I didn't want you to think I'm not smart."

"Skye you hacked into SHIELD from your van. I know you're smart. Alright, so we won't do written tests or quizzes anymore. I'll find another way to help you retain information. Now what else?"

Skye looked up now angry, "Why didn't you tell me about Ward?"

May continued to look at Skye, she didn't say a word for a few moments before she stood up. "Stand up." Skye did as she was told, "Follow me." May said leading them over to the mats. She turned to face Skye, "Come on," she said standing in a defensive stance.

Skye angrily charged at May. All of May's guidance about combat forgotten. She only saw red. May easily defended herself, blocking Skye's wild unruling jabs and punches. She caught Skye's fist and flipped her onto her back. Skye gasped as May held her down, "This is why I didn't tell you about Ward."

"I deserve to know!"

"Skye take deep breaths." May ordered.

"Let me up!"

"Skye do your breathing! Now!"

Skye whimpered and struggled to get up, but when she realized she couldn't escape May's grasp she started to do her breathing.

May watched Skye begin to calm. When her breathing returned to normal May let Skye up. "Listen to me. Being a Field Agent or Specialist means you need to have emotional control at all times, especially during missions, during combat, and when you're captured. We need to know what triggers us mentally and emotionally so when we run into them during missions we can expect how we'll react and know how to use our emotions properly."

"I can't be ice cold like you."

"Right before I fought Ward, I told you that I do feel. I told you that I mine it, and use it properly. If you were fighting a Hydra Agent or Ward or anyone else just like you did with me, they would have killed you because your logical side of your brain was not on. You can have emotions Skye, I'm trying to teach you how to control them, so you can use them in the Field, and so no one can take advantage of you."

Skye looked down, "I'm sorry."

"I know. You don't have to be sorry, Skye. You responded how any normal person would. You reacted because you the lack the emotional discipline. That's what I'm going to train you."

"But you hide things from me."

"Skye, I don't hide things from you. I understand that you're upset with me right now, that's OK, you're going to get frustrated with me, because I'm going to push you during the day. I am not doing this to cause you damage, but I am going to make you the Field Agent that you want to be. So do you trust me to be your S.O.?"

Skye gulped and looked down, "It feels like you lied to me."

"I know you feel betrayed by me." May told her gently, "As you just demonstrated, you weren't emotionally prepared to know that Ward was here. It affected your training and it made you act out in rage."

"Why is he here?"

"We're using him to learn intel about Hydra. I wish he wasn't here. I hate that he's here, but we're in the dark and we need every resource available to us to learn about the enemy. That's all he is, he's an asset."

Skye sat quietly for a minute, "Are you still going to train me?"

"Yes I am. You haven't disappointed me Skye."

Skye looked unsure, "Promise?"

"Promise. Are you feeling a little better now?" Skye nodded, "Good, it's 2:30, but I know you're extremely overwhelmed. You're done training today. Go cool down, make sure you ice your shins." May stood up and held out her hand.

"OK." Skye looked up at her and took May's hand, "I trust you May." she whispered.

* * *

><p>Author's Note: I'm really trying to write everyone in character, while showing the subtle changes to the team ever since SHIELD had fallen. I know May doesn't say much, but because Skye is different this most agents due to her upbringing, I'd think May had to take a different approach in training her. In the episodes we've already seen her warmer towards Skye, Fitz, and Jemma.<p> 


End file.
